I am using vanilla sources to build a debian RT custom kernel using make-kpkg.Compiling goes very nice and ends up with a deb kernel package but make-kpkg does't generate initrd using --initrd option! I had to generete it by hand with update-initrams and the put the corresponding line to menu.lst in order to boot.

I usually run latest stable vanilla releases and never experienced that problem with make-kpkg.